MmuINT0039724 @ mm10
Intron Retention
Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:63324772-63325211:+
Coord C1 exon
chr4:63324772-63324789
Coord A exon
chr4:63324790-63325175
Coord C2 exon
chr4:63325176-63325211
Length
386 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
GTCTCTTCTTTCTTCCACAGGGT
3' ss Score
12.85
Exon sequences
Seq C1 exon
GGACTGCAAGGCCCAAGG
Seq A exon
GTAAGTAGAGTGGGTGTGAGGACTTGGGACTGGGGACAGGAGTGGGGGGTTCTCGGGCTCTCCTTTCCACAGTGACACCTTTCTATCTCTGTCTCTCTCTCTCTCTGTCTTCTCTCTCTGTCTGTCTTCTCTCTGTGTCTCTGTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTCTGTGTGTCTGTGTGTGTGTCTCTCTCTCTGTGTATGTGTGTCTGTGTCTGTGTGTGTCTGTGTGTGTCTCTCTCTCTGACATTCTTTTTCTCTGTACCCTTCCCCAGGGGAACATCATCTCTGGGTCTGGGTAGGACAAAAGACAGCCTGGGTAAGGAACTGTCCAGAGCTGACTGTCTCTTCTTTCTTCCACAG
Seq C2 exon
GGTCCTCCTGGTCCAAGGGGCCGGCCAGGTCCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672:ENSMUST00000036300:54
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(7.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types